Multiple sequence alignment - TraesCS3B01G284200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G284200 chr3B 100.000 2258 0 0 1 2258 455066131 455063874 0.000000e+00 4170.0
1 TraesCS3B01G284200 chr5B 98.099 789 11 2 1473 2258 658766752 658765965 0.000000e+00 1371.0
2 TraesCS3B01G284200 chr2B 97.719 789 15 1 1473 2258 91052874 91053662 0.000000e+00 1354.0
3 TraesCS3B01G284200 chr2B 97.338 789 18 1 1473 2258 91062538 91063326 0.000000e+00 1338.0
4 TraesCS3B01G284200 chr2B 97.085 789 19 2 1473 2257 91056062 91056850 0.000000e+00 1327.0
5 TraesCS3B01G284200 chr2B 96.701 788 23 1 1473 2257 91059351 91060138 0.000000e+00 1308.0
6 TraesCS3B01G284200 chr6B 96.578 789 24 1 1473 2258 462170873 462171661 0.000000e+00 1304.0
7 TraesCS3B01G284200 chrUn 96.914 713 19 1 1473 2182 411185830 411185118 0.000000e+00 1192.0
8 TraesCS3B01G284200 chrUn 96.634 713 21 1 1473 2182 411184402 411183690 0.000000e+00 1181.0
9 TraesCS3B01G284200 chr3D 91.197 852 50 9 1 832 354621066 354620220 0.000000e+00 1134.0
10 TraesCS3B01G284200 chr3D 94.028 653 28 3 831 1473 354620178 354619527 0.000000e+00 979.0
11 TraesCS3B01G284200 chr3A 93.529 680 42 2 616 1294 473213393 473212715 0.000000e+00 1011.0
12 TraesCS3B01G284200 chr3A 91.795 585 25 11 48 612 473216720 473216139 0.000000e+00 793.0
13 TraesCS3B01G284200 chr3A 96.053 76 3 0 1337 1412 473212718 473212643 8.470000e-25 124.0
14 TraesCS3B01G284200 chr3A 90.909 55 0 3 1419 1473 473212465 473212416 4.020000e-08 69.4
15 TraesCS3B01G284200 chr7D 88.619 782 86 1 1480 2258 131448184 131448965 0.000000e+00 948.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G284200 chr3B 455063874 455066131 2257 True 4170.00 4170 100.00000 1 2258 1 chr3B.!!$R1 2257
1 TraesCS3B01G284200 chr5B 658765965 658766752 787 True 1371.00 1371 98.09900 1473 2258 1 chr5B.!!$R1 785
2 TraesCS3B01G284200 chr2B 91052874 91063326 10452 False 1331.75 1354 97.21075 1473 2258 4 chr2B.!!$F1 785
3 TraesCS3B01G284200 chr6B 462170873 462171661 788 False 1304.00 1304 96.57800 1473 2258 1 chr6B.!!$F1 785
4 TraesCS3B01G284200 chrUn 411183690 411185830 2140 True 1186.50 1192 96.77400 1473 2182 2 chrUn.!!$R1 709
5 TraesCS3B01G284200 chr3D 354619527 354621066 1539 True 1056.50 1134 92.61250 1 1473 2 chr3D.!!$R1 1472
6 TraesCS3B01G284200 chr3A 473212416 473216720 4304 True 499.35 1011 93.07150 48 1473 4 chr3A.!!$R1 1425
7 TraesCS3B01G284200 chr7D 131448184 131448965 781 False 948.00 948 88.61900 1480 2258 1 chr7D.!!$F1 778


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
898 3724 0.178992 TGGAGCCAAACCCACTCTTG 60.179 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 11214 2.418197 CGCGAAAACTCATTCCTCCCTA 60.418 50.0 0.0 0.0 0.0 3.53 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.877178 TGTGGAAAAAGCTTTAATTCAGTAAAA 57.123 25.926 20.02 1.78 0.00 1.52
64 65 3.153919 TGGAATGCCTGTCTTGTAAACC 58.846 45.455 0.00 0.00 34.31 3.27
92 93 2.676463 GCCTGTTTGTGCTTGGTTTTCA 60.676 45.455 0.00 0.00 0.00 2.69
103 104 4.217550 TGCTTGGTTTTCAATGGTACTAGC 59.782 41.667 0.00 0.00 34.45 3.42
160 182 4.036144 GGAGAAATGCTGCTTAAGATGTCC 59.964 45.833 6.67 0.00 31.32 4.02
173 195 3.611766 AGATGTCCTCCTGTTAAACCG 57.388 47.619 0.00 0.00 0.00 4.44
178 200 1.000060 TCCTCCTGTTAAACCGTGTCG 60.000 52.381 0.00 0.00 0.00 4.35
179 201 1.000060 CCTCCTGTTAAACCGTGTCGA 60.000 52.381 0.00 0.00 0.00 4.20
181 203 1.142474 CCTGTTAAACCGTGTCGACC 58.858 55.000 14.12 3.43 0.00 4.79
462 484 1.078214 TGTGCTCTGCATACTGGCC 60.078 57.895 0.00 0.00 41.91 5.36
543 565 6.822676 TGAAATCATTTCCACAATTATTGGCC 59.177 34.615 7.68 0.00 38.90 5.36
553 575 5.490159 CACAATTATTGGCCTTCCACATTT 58.510 37.500 3.32 0.00 43.33 2.32
583 605 1.242076 CTGAGTTGCTTGGAGTTGGG 58.758 55.000 0.00 0.00 0.00 4.12
584 606 0.843309 TGAGTTGCTTGGAGTTGGGA 59.157 50.000 0.00 0.00 0.00 4.37
585 607 1.239347 GAGTTGCTTGGAGTTGGGAC 58.761 55.000 0.00 0.00 0.00 4.46
591 613 0.607489 CTTGGAGTTGGGACTGCTGG 60.607 60.000 0.00 0.00 43.87 4.85
612 634 4.277174 TGGTGATGCGTGTTTTTCTGTTAT 59.723 37.500 0.00 0.00 0.00 1.89
613 635 4.616802 GGTGATGCGTGTTTTTCTGTTATG 59.383 41.667 0.00 0.00 0.00 1.90
626 3390 3.073678 TCTGTTATGCATGTGCTCGTTT 58.926 40.909 10.16 0.00 42.66 3.60
666 3431 3.161866 ACTTGGTATTTTGCGTGGGAAT 58.838 40.909 0.00 0.00 0.00 3.01
778 3561 3.627395 AGTATTCCGTGAGCATCCAAA 57.373 42.857 0.00 0.00 0.00 3.28
799 3582 2.879646 AGAAATTTAACGCCACGGAACA 59.120 40.909 0.00 0.00 0.00 3.18
824 3607 6.811253 ATTTAACAGTCAAAATCTACGCCA 57.189 33.333 0.00 0.00 0.00 5.69
898 3724 0.178992 TGGAGCCAAACCCACTCTTG 60.179 55.000 0.00 0.00 0.00 3.02
903 3729 1.754226 GCCAAACCCACTCTTGACAAA 59.246 47.619 0.00 0.00 0.00 2.83
952 3778 2.413310 ACCGGTATAAAACCCAGCTG 57.587 50.000 4.49 6.78 46.62 4.24
995 3823 1.574702 CGAAGAAACCAAGACCCCGC 61.575 60.000 0.00 0.00 0.00 6.13
996 3824 0.250770 GAAGAAACCAAGACCCCGCT 60.251 55.000 0.00 0.00 0.00 5.52
1018 3846 2.362369 ATGTCAGTCGGCCAGAGGG 61.362 63.158 2.24 0.00 37.18 4.30
1029 3857 3.003173 CAGAGGGCCACCGAGGAA 61.003 66.667 6.18 0.00 43.47 3.36
1095 3923 2.359169 CCGCCTCTTGTCTGGCCTA 61.359 63.158 3.32 0.00 45.90 3.93
1098 3926 1.903877 GCCTCTTGTCTGGCCTAGCA 61.904 60.000 3.32 0.00 43.11 3.49
1276 4104 0.400213 ATTCGGCTTGGACTGGACAA 59.600 50.000 0.00 0.00 0.00 3.18
1405 4233 9.864034 CATTCATTAATTCGTTGTATGTACTCC 57.136 33.333 0.00 0.00 0.00 3.85
1437 4436 7.685481 TGTCTCTCCCATTCTTAACAAATACA 58.315 34.615 0.00 0.00 0.00 2.29
1442 4441 7.769044 TCTCCCATTCTTAACAAATACAGTAGC 59.231 37.037 0.00 0.00 0.00 3.58
1648 7835 1.398958 GGTTTGCAAAGGCCTCACCA 61.399 55.000 13.26 0.00 43.14 4.17
1738 11214 1.967319 ACTTGCATCACCGAAGTGTT 58.033 45.000 0.00 0.00 44.83 3.32
1750 11226 2.500098 CCGAAGTGTTAGGGAGGAATGA 59.500 50.000 0.00 0.00 0.00 2.57
1785 11261 3.411446 TGAGTTATTCAACCTGGCACTG 58.589 45.455 0.00 0.00 35.05 3.66
2171 14837 0.257328 TTGAATATCCCCTTGCGCCA 59.743 50.000 4.18 0.00 0.00 5.69
2173 14839 0.465460 GAATATCCCCTTGCGCCACA 60.465 55.000 4.18 0.00 0.00 4.17
2174 14840 0.033601 AATATCCCCTTGCGCCACAA 60.034 50.000 4.18 0.00 36.62 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.279456 GGTTTACAAGACAGGCATTCCATTT 60.279 40.000 0.00 0.00 33.74 2.32
42 43 3.763897 GGTTTACAAGACAGGCATTCCAT 59.236 43.478 0.00 0.00 33.74 3.41
64 65 3.673484 CACAAACAGGCAGGGGCG 61.673 66.667 0.00 0.00 42.47 6.13
92 93 4.385310 GGACCATTTCCAGCTAGTACCATT 60.385 45.833 0.00 0.00 45.10 3.16
160 182 2.056577 GTCGACACGGTTTAACAGGAG 58.943 52.381 11.55 0.00 0.00 3.69
173 195 4.813296 AGAAAACAAATGAGGTCGACAC 57.187 40.909 18.91 11.25 0.00 3.67
178 200 9.565213 CATTAGATCAAGAAAACAAATGAGGTC 57.435 33.333 0.00 0.00 0.00 3.85
179 201 8.526147 CCATTAGATCAAGAAAACAAATGAGGT 58.474 33.333 0.00 0.00 0.00 3.85
181 203 9.918630 AACCATTAGATCAAGAAAACAAATGAG 57.081 29.630 0.00 0.00 0.00 2.90
208 230 4.473444 TGACCTGGAAAGCAAGAAGAATT 58.527 39.130 0.00 0.00 0.00 2.17
462 484 9.535878 GATATAGAACCTACTGAGAAAACTTGG 57.464 37.037 0.00 0.00 0.00 3.61
543 565 7.439056 ACTCAGCAAAAACAATAAATGTGGAAG 59.561 33.333 0.00 0.00 42.99 3.46
553 575 5.049167 CCAAGCAACTCAGCAAAAACAATA 58.951 37.500 0.00 0.00 36.85 1.90
583 605 1.230635 AACACGCATCACCAGCAGTC 61.231 55.000 0.00 0.00 0.00 3.51
584 606 0.819259 AAACACGCATCACCAGCAGT 60.819 50.000 0.00 0.00 0.00 4.40
585 607 0.311790 AAAACACGCATCACCAGCAG 59.688 50.000 0.00 0.00 0.00 4.24
591 613 4.088496 GCATAACAGAAAAACACGCATCAC 59.912 41.667 0.00 0.00 0.00 3.06
612 634 1.069296 GCACTTAAACGAGCACATGCA 60.069 47.619 6.64 0.00 45.16 3.96
613 635 1.197721 AGCACTTAAACGAGCACATGC 59.802 47.619 0.00 0.00 42.49 4.06
648 3413 5.244178 ACTTAAATTCCCACGCAAAATACCA 59.756 36.000 0.00 0.00 0.00 3.25
655 3420 3.759086 TGCATACTTAAATTCCCACGCAA 59.241 39.130 0.00 0.00 0.00 4.85
778 3561 2.879646 TGTTCCGTGGCGTTAAATTTCT 59.120 40.909 0.00 0.00 0.00 2.52
799 3582 7.653647 TGGCGTAGATTTTGACTGTTAAATTT 58.346 30.769 0.00 0.00 0.00 1.82
824 3607 5.368989 GTCCAAGGAATCGACTTTCCATAT 58.631 41.667 17.84 3.50 46.40 1.78
898 3724 2.589442 TGTCCCGCACGGTTTGTC 60.589 61.111 8.49 0.00 0.00 3.18
952 3778 5.221244 GGTGAAATTGTGGATTATAGGTGGC 60.221 44.000 0.00 0.00 0.00 5.01
995 3823 2.821366 GGCCGACTGACATGCCAG 60.821 66.667 7.56 7.56 43.46 4.85
1069 3897 0.824759 GACAAGAGGCGGTCATACCT 59.175 55.000 0.00 0.00 39.65 3.08
1276 4104 2.938354 GCTGTGAAGTGCCATCAGT 58.062 52.632 0.00 0.00 0.00 3.41
1349 4177 4.521639 TGAAATCTTCAGCAGCATCTTGTT 59.478 37.500 0.00 0.00 34.08 2.83
1388 4216 5.769484 AGATCGGAGTACATACAACGAAT 57.231 39.130 10.65 3.03 39.02 3.34
1405 4233 5.720371 AAGAATGGGAGAGACATAGATCG 57.280 43.478 0.00 0.00 0.00 3.69
1437 4436 3.768757 TGCTGCCCAAATTTTATGCTACT 59.231 39.130 0.00 0.00 0.00 2.57
1738 11214 2.418197 CGCGAAAACTCATTCCTCCCTA 60.418 50.000 0.00 0.00 0.00 3.53
1750 11226 5.637810 TGAATAACTCAAGATCGCGAAAACT 59.362 36.000 15.24 10.56 0.00 2.66
1979 11455 5.878406 ATCTTCCCAAATCGAGATAGTGT 57.122 39.130 0.00 0.00 0.00 3.55
2171 14837 2.760092 CGAAAATCATCACCCCCATTGT 59.240 45.455 0.00 0.00 0.00 2.71
2173 14839 3.290710 CTCGAAAATCATCACCCCCATT 58.709 45.455 0.00 0.00 0.00 3.16
2174 14840 2.936202 CTCGAAAATCATCACCCCCAT 58.064 47.619 0.00 0.00 0.00 4.00



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.